Charlotta’s paper

Figures for Paper

DGE summary

  • differences between fetal and adult cells in general

DGE performed after removing outliers illustrated in the tSNA/PCA/UMAPs below

Volcano plot

  • HSC like cells, IL7R prog and proB from adult BM vs w12-13, w8-10 and CS samples
  • exclude CS16 for now

GO

  • combine all changed genes between fetal and adult

tryHyper

Laurenti Muschen using ProB only

CMP

Laurenti Muschen using IL7R only

NO assotiation found with Laurenti gene lists.

Try with HALLMARK

GSEA with Adult V fetal (in general)

## v7.0.1
## Downloading genesets to...
## /tmp/Rtmp7fNmKo
## - C1 -> 299 Gene Sets 
## - C2.CGP -> 3302 Gene Sets 
## - C2.CP -> 29 Gene Sets 
## - C2.CP.BIOCARTA -> 289 Gene Sets 
## - C2.CP.KEGG -> 186 Gene Sets 
## - C2.CP.PID -> 196 Gene Sets 
## - C2.CP.REACTOME -> 1499 Gene Sets 
## - C3.MIR -> 221 Gene Sets 
## - C3.TFT -> 610 Gene Sets 
## - C4.CGN -> 427 Gene Sets 
## - C4.CM -> 431 Gene Sets 
## - C5.BP -> 7350 Gene Sets 
## - C5.CC -> 1001 Gene Sets 
## - C5.MF -> 1645 Gene Sets 
## - C6 -> 189 Gene Sets 
## - C7 -> 4872 Gene Sets 
## - H -> 50 Gene Sets

KEGG

Reactome

UMAP/tSNE plot or PCA plot

  • only IL7R and proB from BM and all fetal stages
  • exclude CB, do with and without CS16

tSNE

PCA

UMAP

Take out CD34+CD38-CD45RA-

tSNE

PCA

UMAP

IL7R only

tSNE

PCA

DGE performed after HSCs taken out

Volcano plot

IL7R prog and proB from adult BM vs w12-13, w8-10 and CS samples - exclude CS16 for now

GO

  • combine all changed genes between fetal and adult

tryHyper

## v7.0.1
## Downloading genesets to...
## /tmp/Rtmp7fNmKo
## - C1 -> 299 Gene Sets 
## - C2.CGP -> 3302 Gene Sets 
## - C2.CP -> 29 Gene Sets 
## - C2.CP.BIOCARTA -> 289 Gene Sets 
## - C2.CP.KEGG -> 186 Gene Sets 
## - C2.CP.PID -> 196 Gene Sets 
## - C2.CP.REACTOME -> 1499 Gene Sets 
## - C3.MIR -> 221 Gene Sets 
## - C3.TFT -> 610 Gene Sets 
## - C4.CGN -> 427 Gene Sets 
## - C4.CM -> 431 Gene Sets 
## - C5.BP -> 7350 Gene Sets 
## - C5.CC -> 1001 Gene Sets 
## - C5.MF -> 1645 Gene Sets 
## - C6 -> 189 Gene Sets 
## - C7 -> 4872 Gene Sets 
## - H -> 50 Gene Sets

KEGG

Reactome